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<h1>Export/Submit to GNPS-FBMN</h1>

<h2>Description</h2>
<p>
    The GNPS Export/Submit module exports all files needed for <strong>Feature-Based Molecular Networking</strong> on the <a href="http://gnps.ucsd.edu/">GNPS web-platform</a>. 
    This includes the <strong>feature quantification table</strong> (CSV file) and the <strong>MS/MS spectral summary</strong> (.MGF file) with representative MS/MS spectra for the row in Aligned Peaklist.
    Optionally, a new GNPS job is submitted. This job can either be directly linked with a GNPS user profile (username and password are optional) or can be cloned into a personal GNPS account later on.</p>
<p><strong>IMPORTANT for the "Submit to GNPS" option:</strong></p>
<ul>
<li>The password is sent <strong>without encryption </strong> (until the server has moved to its final location with https).</li>
<li>The input files uploaded to GNPS with the "Submit to GNPS" option are not saved on your GNPS user account. These files are&nbsp;deleted on monthly basis, which prevent futur cloning of the job and retrieval of the files. Use the <a href="https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/">"standard" interface of the FBMN</a> for persistant jobs and more options.</li>
</ul>
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<h2>Instructions</h2>
<p>
    Run this method on any Aligned Peak List. MS/MS spectra need to be associated to the features (usually done in the peak deconvolution step).
</p>


<h2>Parameters</h2>
<dl>
    <dt>Filename</dt>
    <dd>Base name for the output files</dd>
    
    <dt>Mass list</dt>
    <dd>Select the masslist that contains MS2 scans (and MS1 for the Merge MS/MS option)</dd>
    
    <dt>Merge MS/MS (Experimental)</dt>
    <dd>The Merge MS/MS option enables to merge MS2 spectra associated to an LC-MS feature (or LC-MS peak) in one representative MS/MS spectrum. In this mode, the precursor ion purity is evaluated using MS1 scans, and the MS2 spectra are merged using various options. See our preprint for more informations.</dd>
    
    <dt>Filter rows</dt>
    <dd>Limit the exported rows to be included in the MS/MS spectral summary file (.MGF). Default is "ONLY WITH MS2 or ANNOTATION"</dd>

    <dt>Submit to GNPS</dt>
    <dd>Directly submit a job to GNPS for rapid analysis. This job can either be directly linked with a GNPS user profile (username and password are optional) or can be cloned into a personal GNPS account later on. IMPORTANT: files are not served on the GNPS. See above disclaimer.</p></dd>
    
    <dt>Open folder</dt>
    <dd>Opens the folder containing the output files</dd>
</dl>

<h2>Documentation</h2>
<p>
    Please refer to the following documentation for a detailed tutorial:
    <ul>    
        <li>If you use the <em>GNPS Export/Submit</em> please cite:
            <ul>
                <li>our preprint: Nothias et al.: <a href="https://www.biorxiv.org/content/10.1101/812404v1">bioRxiv 812404 (2019)</a></li>
                <li>the <a href="http://gnps.ucsd.edu/">GNPS</a> paper: Wang et al.: <a href="https://www.nature.com/nbt/journal/v34/n8/full/nbt.3597.html">Nature Biotechnology 34.8 (2016): 828-837</a><a href="http://gnps.ucsd.edu/">.</a></li>
                <li>and the MZmine paper: Pluskal et al.: <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-395">BMC Bioinformatics, 11, 395 (2010)</a></li>
            </ul>
        </li>
        <li><a href="https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/">See the documentation</a> about FBMN with MZmine on <a href="https://ccms-ucsd.github.io/GNPSDocumentation">GNPS</a>, and how to perform molecular networking, MS/MS spectral library search, and benefit from other tools available in GNPS environment.</li>
        <li>Or check out the <a href="https://www.youtube.com/watch?v=vFcGG7T_44E&list=PL4L2Xw5k8ITzd9hx5XIP94vFPxj1sSafB&index=4&t=146s">youtube playlist</a> on important steps for FBMN within MZmine and direct submission of the data to GNPS.</li>
    </ul>
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